75 Works

Research Life Cycle: Exploring Credibility of Metrics and Value in a New Era of eScholarship that Supports Grey Literature

Julia Gelfand & Anthony Lin
The fundamental components of the research process are defined by academic tradition, discipline and its participants. Traditional scholarship has now evolved into eScholarship with emerging technologies providing new methods of innovation and new ways of handling classical research processes. This revised research life cycle not only incorporates the established parts of the research chain, from discovery, gathering, and creating, but now has added phases of citing, sharing, preserving and archiving. There are quantifiable elements that...

Global gradients in intraspecific variation in vegetative and floral traits are partially associated with climate and species richness

Jonas Kuppler, Cécile H. Albert, Gregory M. Ames, W. Scott Armbruster, Gerhard Boenisch, Florian C. Boucher, Diane R. Campbell, Liedson T. Carneiro, Eduardo Chacón-Madrigal, Brian J. Enquist, Carlos R. Fonseca, José M. Gómez, Antoine Guisan, Pedro Higuchi, Dirk N. Karger, Jens Kattge, Michael Kleyer, Nathan J. B. Kraft, Anne-Amélie C. Larue-Kontić, Amparo Lázaro, Martin Lechleitner, Deirdre Loughnan, Vanessa Minden, Ülo Niinemets, Gerhard E. Overbeck … & Robert R. Junker
Aim Intraspecific trait variation (ITV) within natural plant communities can be large, influencing local ecological processes and dynamics. Here, we shed light on how ITV in vegetative and floral traits responds to large-scale abiotic and biotic gradients (i.e. climate and species richness). Specifically, we tested if associations of ITV with temperature, precipitation and species richness were consistent with any of from four hypotheses relating to stress-tolerance and competition. Furthermore, we estimated the degree of correlation...

Data from: The rhythm of attention: perceptual modulation via rhythmic entrainment is lowpass and attention mediated

Kourosh Saberi, Haleh Farahbod & Gregory Hickok
Modulation patterns are known to carry critical predictive cues to signal detection in complex acoustic environments. The current study investigated the persistence of masker modulation effects on post-modulation detection of probe signals. Hickok et al. (2015) demonstrated that thresholds for a tone pulse in stationary noise follow a predictable periodic pattern when preceded by a 3-Hz amplitude modulated masker. They found entrainment of detection patterns to the modulation envelope lasting for approximately 2 cycles after...

The direct and indirect effects of environmental toxicants on the health of bumble bees and their microbiomes

Jason Rothman, Kaleigh Russell, Laura Leger, Quinn McFredderick & Peter Graystock
Bumble bees (Bombus spp.) are important and widespread insect pollinators, but the act of foraging on flowers can expose them to harmful pesticides and chemicals such as oxidizers and heavy metals. How these compounds directly influence bee survival and indirectly affect bee health via the gut microbiome is largely unknown. As toxicants in floral nectar and pollen take many forms, we explored the genomes of bee-associated microbes for their potential to detoxify cadmium, copper, selenate,...

Identifying mechanisms for successful ecological restoration with salvaged topsoil in coastal sage scrub communities

Mia Maltz & Katharina Schmid
Although above-ground metrics remain the standard, restoring functional ecosystems should promote both above- and belowground biotic communities. Restoration using salvaged soil — removal and translocation of topsoil from areas planned for development, with subsequent deposition at degraded sites — is an alternative to traditional methods. Salvaged soil contains both seed and spore banks, which may holistically augment restoration. Salvaged soil methods may reduce non-native germination by burying non-native seeds, increase native diversity by adding native...

Data from: Evapotranspiration response to multiyear dry periods in the semiarid western United States

Joseph Rungee, Roger Bales, Michael Goulden, Gerald Flerchinger, Greg Barron-Gafford & Xiande Meng
Analysis of measured evapotranspiration shows that subsurface plant‐accessible water storage (PAWS) can sustain evapotranspiration through multiyear dry periods. Measurements at 25 flux tower sites in the semiarid western United States, distributed across five land cover types, show both resistance and vulnerability to multiyear dry periods. Average (±standard deviation) evapotranspiration ranged from 660 ± 230 mm yr−1 (October–September) in evergreen needleleaf forests to 310 ± 200 mm yr−1 in grasslands and shrublands. More than 52% of...

Fatigue resistant jaw muscles facilitate long-lasting courtship behavior in the southern alligator lizard (Elgaria multicarinata)

A. Kristopher Lappin, Allyn Nguyen, Jordan Balaban, Emanuel Azizi & Robert Talmadge
The southern alligator lizard (Elgaria multicarinata) exhibits a courtship behavior during which the male firmly grips the female’s head in his jaws for many hours at a time. This extreme behavior counters the conventional wisdom that reptile muscles are fast to fatigue and incapable of powering high endurance behaviors. We conducted in situ experiments in which the jaw-adductor muscles of lizards were stimulated directly while bite force was measured simultaneously with a force transducer. Fatigue...

Best-practice forestry management delivers diminishing returns for coral reefs with increased land-clearing

Amelia Wenger, Daniel Harris, Samuel Weber, Ferguson Vaghi, Yashika Nand, Waisea Naisilisili, Alec Hughes, Jade Delevaux, Carissa Klein, James Watson, Peter Mumby & Stacy Jupiter
Protection of coastal ecosystems from deforestation may be the best way to protect coral reefs from sediment runoff. However, given the importance of generating economic activities for coastal livelihoods, the prohibition of development is often not feasible. In light of this, logging codes-of-practice have been developed to mitigate the impacts of logging on downstream ecosystems. However, no studies have assessed whether managed land-clearing can occur in tandem with coral reef conservation goals. This study quantifies...

More than meets the eye: syntopic and morphologically similar mangrove killifish species show different mating systems and patterns of genetic structure along the Brazilian coast

Waldir Berbel-Filho, Andrey Tatarenkov, Helder Espírito-Santo, Mateus Lira, Carlos De Leaniz, Sergio Lima & Sofia Consuegra
Different mating systems can strongly affect the extent of genetic diversity and population structure among species. Given the increased effects of genetic drift on reduced population size, theory predicts that species undergoing self-fertilization should have greater population structure than outcrossed species, however demographic dynamics may affect this scenario. The mangrove killifish clade is composed of the two only known examples of self-fertilising species among vertebrates (Kryptolebias marmoratus and K. hermaphroditus). A third species in this...

Hamiltonian patterns of age-dependent adaptation to novel environments

Grant Rutledge, Larry Cabral, Brandon Kuey, Joshua Lee, Laurence Mueller & Michael Rose
Our intuitive understanding of adaptation by natural selection is dominated by the power of selection at early ages in large populations. Yet, as the forces of natural selection fall with adult age, we expect adaptation to be attenuated with age. Explicit simulations of age-dependent adaptation suggest that populations adapt to a novel environment quickly at early ages, but only slowly and incompletely at later adult ages. Experimental tests for age-dependent adaptation to a novel diet...

Model code for reconstructing biomass burning emissions from ice core records of acetylene, ethane, and methane

Melinda Nicewonger, Murat Aydin & Eric Saltzman
Biomass burning emissions of trace gases are inferred from ice core levels of acetylene, ethane, methane and its stable isotopes over the last 1,000 years (Nicewonger et al., 2018, 2020). In Nicewonger et al. 2020 JGR-A, we attempt to reconcile the individual biomass burning records from each trace gas into a single fire history of dry matter burned over the last 1,000 years. We find that temporal trends in fire inferred from the three trace...

Proposed managed aquifer recharge projects in California groundwater sustainability plans

Nicola Ulibarri & Nataly Escobedo Garcia
This dataset contains the text description of Managed Aquifer Recharge (MAR) projects proposed by Groundwater Sustainability Agencies in California to comply with the requirements of the Sustainable Groundwater Management Act (SGMA). The dataset includes projects proposed in the Groundwater Sustainability Plans submitted in 2020 for critically-overdrafted basins.

Antagonistic effects of temperature and dissolved organic carbon on fish growth in California mountain lakes

Celia C. Symons, Marika A. Schulhof, Hamanda B. Cavalheri & Jonathan B. Shurin
Resources and temperature play major roles in determining biological production in lake ecosystems. Lakes have been warming and ‘browning’ over recent decades due to climate change and increased loading of terrestrial organic matter. Conflicting hypotheses and evidence have been presented about whether these changes will increase or decrease fish growth within lakes. Most studies have been conducted in low-elevation lakes where terrestrially derived carbon tends to dominate over carbon produced within lakes. Understanding how fish...

Evapotranspiration data from eddy-covariance flux-tower measurements and Landsat imagery in California’s Sierra Nevada from 1985 to 2019

Qin Ma, Roger Bales, Joseph Rungee, Martha Conklin, Xiande Meng & Michael Goulden
The gridded annual evapotranspiration (ET) from 1985 to 2019 were calculated based on the correlations between eddy-covariance flux-tower measurements of annual evapotranspiration and satellite imagery derived Normalized Difference Vegetation Index (NDVI). Annual ET observations from 12 flux-towers across the Sierra Nevada and Southern California were collected from 2001 to 2016, resulting 97 site-years of ET observations in five main vegetation types (Evergreen Needleleaf Forest, Grasslands, Mixed Forest, Open Shrublands, and Woody Savannas). The NDVI was...

Data from: Testing trade-offs and the dominance-impoverishment rule among ant communities

Julie K. Sheard, Annika S. Nelson, Jeppe Berggreen, Raphael Boulay, Robert R. Dunn & Nathan J. Sanders
Aim: Ant communities are believed to be structured by competition, with dominant species competitively excluding subordinates (the dominance-impoverishment rule). However, a high number of seemingly similar species coexist, possibly due to interspecific trade-offs. Here, we examine the evidence for the dominance-impoverishment rule across a broad latitudinal gradient and explore whether trade-offs explain coexistence within and among ant communities. Location: 40 sites in 19 countries across Europe, western North America and northern South America. Taxon: Formicidae....

Coastal urbanization influences human pathogens and microdebris contamination in seafood

Raechel Littman, Evan Fiorenza, Amelia Wenger, Kathryn Berry, Jeroen Van De Water, Lily Nguyen, Soe Tint Aung, Daniel Parker, Douglas Rader, C. Drew Harvell & Joleah Lamb
Seafood is one of the leading imported products implicated in foodborne outbreaks worldwide. Coastal marine environments are being increasingly subjected to reduced water quality from urbanization and leading to contamination of important fishery species. Given the importance of seafood exchanged as a global protein source, it is imperative to maintain seafood safety worldwide. To illustrate the potential health risks associated with urbanization in a coastal environment, we use next-generation high-throughput amplicon sequencing of the 16S...

A compilation of canopy leaf inclination angle measurements across plant species and biome types

César Hinojo-Hinojo & Michael Goulden
The inclination angle of leaves in plant canopies is important for a range of land ecosystem processes, including radiation absorption from vegetation, land surface reflectance, microclimate, and photosynthetic CO2 uptake. While inclination angles of leaves have been measured for decades, such measurements remain scattered in the scientific literature, and the actual variation of leaf inclination angles across land ecosystems remains poorly understood and quantified. We compiled a dataset of previously published field measurements of mean...

An electrophysiological marker of arousal level in humans

Janna Lendner, Randolph Helfrich, Bryce Mander, Luis Romundstad, Jack Lin, Matthew Walker, Pal Larsson & Robert Knight
Deep non-rapid eye movement sleep (NREM) and general anesthesia with propofol are prominent states of reduced arousal linked to the occurrence of synchronized oscillations in the electroencephalogram (EEG). Although rapid eye movement (REM) sleep is also associated with diminished arousal levels, it is characterized by a desynchronized, 'wake-like' EEG. This observation implies that reduced arousal states are not necessarily only defined by synchronous oscillatory activity. Using intracranial and surface EEG recordings in four independent data...

The Ubiquity of Grey Literature in a Connected Content Context

Julia Gelfand
Ubiquitous or pervasive computing has become a new paradigm in computer science and networking and seeks to embed computers into all functions of daily life, where the technology may be invisible. This "calm technology" allows for some powerful new products and ways of doing things. In the library, publishing, and information arenas this may mean potentially transforming the bibliographic organization and how scholars find and use information. The social and cultural enhancements ubiquitous computing offers...

Crosslinguistic Word Orders Enable an Efficient Tradeoff of Memory and Surprisal

Michael Hahn & Richard Futrell

Grey Literature: Taxonomies and Structures for Collection Development

Julia Gelfand
Libraries worldwide have not picked up the pace of addressing where Grey Literature fits in collection policies. This remains rather curious due to the skyrocketing prices of traditional books, journals, databases, and other information resources, and trends to serialize and promote access in perpetuity. Most collection development policies only address resources for which payment has been made, where formal acquisitions or licensing practices are observed. Due to more interest and a commitment to Open Access...

Striated myocyte structural integrity: automated analysis of sarcomeric z-discs

Tessa Altair Morris, Jasmine Naik, Kirby Sinclair Fibbin, Xiangdu Kong, Tohru Kiyono, Kyoko Yokomori & Anna Grosberg
As sarcomeres produce the force necessary for contraction, assessment of sarcomere order is paramount in evaluation of cardiac and skeletal myocytes. The uniaxial force produced by sarcomeres is ideally perpendicular to their z-lines, which couple parallel myofibrils and give cardiac and skeletal myocytes their distinct striated appearance. Accordingly, sarcomere structure is often evaluated by staining for z-line proteins such as alpha-actinin. However, due to limitations of current analysis methods, which require manual or semi-manual handling...

Data from: Complementarity in spatial subsidies of carbon associated with resource partitioning along multiple niche axes

Matthew Bracken
Data support analyses describing the potential for niche partitioning and complementarity in a guild of suspension-feeding rocky shore invertebrates. I focused on the mussels Perna canaliculus, Mytilus galloprovincialis, Aulacomya maoriana, and Xenostrobus pulex, all of which coexist along the coastline of the South Island of New Zealand. I quantified the mussel species’ distributions, both vertically on the shore and within the three-dimensional mussel bed matrix, and used carbon (delta13C) and nitrogen (delta15N) stable isotope ratios...

Data from: Size-resolved chemical composition of sub-20 nm particles from methanesulfonic acid reactions with methylamine and ammonia

Veronique Perraud, Xiaoxiao Li, JingKun Jiang, Barbara Finlayson-Pitts & James Smith
Particle formation in the atmosphere from gas-phase precursors has been observed around the world; however, our fundamental understanding of the key species responsible and mechanisms involved remains uncertain. Recent laboratory studies demonstrated that acid−base reactions involving methanesulfonic acid (CH3SO3H, MSA) and small alkylamines may contribute significantly to new particle formation. To date, most of the investigations have been focused on particle number concentration and size distribution measurements in combination with quantum chemistry predictions of the...

Effects of dominance and female presence on secondary sexual characteristics in male tufted capuchin monkeys (Sapajus apella)

Annika Paukner, Emily Slonecker & Lauren Wooddell
Alpha status may lead to physiological changes that enhance secondary sexual characteristics, which may serve as competitive signals to conspecific males, sexual signals to females, or possibly a combination of both. Here we report measurements of secondary sexual characteristics in captive dominant and subordinate male tufted capuchin monkeys (Sapajus apella) with varying access to females. An adult male (who had previously been subordinate while housed with other males) was paired with an adult female, and...

Registration Year

  • 2020

Resource Types

  • Dataset
  • Text
  • Output Management Plan


  • University of California, Irvine
  • University of California, San Diego
  • Jet Propulsion Lab
  • University of Queensland
  • Grenoble Alpes University
  • University of Arizona
  • University of California, Riverside
  • University of California, Irvine Medical Center
  • University of California, Merced
  • Stanford University